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Cai YD, Chow GK, Hidalgo S, Liu X, Jackson KC, Vasquez CD, Gao ZY, Lam VH, Tabuloc CA, Zheng H, Zhao C, Chiu JC. Alternative splicing of clock transcript mediates the response of circadian clocks to temperature changes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.10.593646. [PMID: 38766142 PMCID: PMC11100826 DOI: 10.1101/2024.05.10.593646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Circadian clocks respond to temperature changes over the calendar year, allowing organisms to adjust their daily biological rhythms to optimize health and fitness. In Drosophila, seasonal adaptations and temperature compensation are regulated by temperature-sensitive alternative splicing (AS) of period (per) and timeless (tim) genes that encode key transcriptional repressors of clock gene expression. Although clock (clk) gene encodes the critical activator of clock gene expression, AS of its transcripts and its potential role in temperature regulation of clock function have not been explored. We therefore sought to investigate whether clk exhibits AS in response to temperature and the functional changes of the differentially spliced transcripts. We observed that clk transcripts indeed undergo temperature-sensitive AS. Specifically, cold temperature leads to the production of an alternative clk transcript, hereinafter termed clk-cold, which encodes a CLK isoform with an in-frame deletion of four amino acids proximal to the DNA binding domain. Notably, serine 13 (S13), which we found to be a CK1α-dependent phosphorylation site, is among the four amino acids deleted in CLK-cold protein. Using a combination of transgenic fly, tissue culture, and in vitro experiments, we demonstrated that upon phosphorylation at CLK(S13), CLK-DNA interaction is reduced, thus decreasing CLK occupancy at clock gene promoters. This is in agreement with our findings that CLK occupancy at clock genes and transcriptional output are elevated at cold temperature, which can be explained by the higher amounts of CLK-cold isoforms that lack S13 residue. This study provides new insights into the complex collaboration between AS and phospho-regulation in shaping temperature responses of the circadian clock.
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Affiliation(s)
- Yao D. Cai
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Gary K. Chow
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Sergio Hidalgo
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Xianhui Liu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Kiya C. Jackson
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Cameron D. Vasquez
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Zita Y. Gao
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Vu H. Lam
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Christine A. Tabuloc
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Haiyan Zheng
- Biological Mass Spectrometry Facility, Robert Wood Johnson Medical School and Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Caifeng Zhao
- Biological Mass Spectrometry Facility, Robert Wood Johnson Medical School and Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Joanna C. Chiu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
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Elgenaidi IS, Spiers JP. Regulation of the phosphoprotein phosphatase 2A system and its modulation during oxidative stress: A potential therapeutic target? Pharmacol Ther 2019; 198:68-89. [PMID: 30797822 DOI: 10.1016/j.pharmthera.2019.02.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 02/15/2019] [Indexed: 02/06/2023]
Abstract
Phosphoprotein phosphatases are of growing interest in the pathophysiology of many diseases and are often the neglected partner of protein kinases. One family member, PP2A, accounts for dephosphorylation of ~55-70% of all serine/threonine phosphosites. Interestingly, dysregulation of kinase signalling is a hallmark of many diseases in which an increase in oxidative stress is also noted. With this in mind, we assess the evidence to support oxidative stress-mediated regulation of the PP2A system In this article, we first present an overview of the PP2A system before providing an analysis of the regulation of PP2A by endogenous inhibitors, post translational modification, and miRNA. Next, a detailed critique of data implicating reactive oxygen species, ischaemia, ischaemia-reperfusion, and hypoxia in regulating the PP2A holoenzyme and associated regulators is presented. Finally, the pharmacological targeting of PP2A, its endogenous inhibitors, and enzymes responsible for its post-translational modification are covered. There is extensive evidence that oxidative stress modulates multiple components of the PP2A system, however, most of the data pertains to the catalytic subunit of PP2A. Irrespective of the underlying aetiology, free radical-mediated attenuation of PP2A activity is an emerging theme. However, in many instances, a dichotomy exists, which requires clarification and mechanistic insight. Nevertheless, this raises the possibility that pharmacological activation of PP2A, either through small molecule activators of PP2A or CIP2A/SET antagonists may be beneficial in modulating the cellular response to oxidative stress. A better understanding of which, will have wide ranging implications for cancer, heart disease and inflammatory conditions.
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Affiliation(s)
- I S Elgenaidi
- Department of Pharmacology and Therapeutics, Trinity College Dublin, Ireland
| | - J P Spiers
- Department of Pharmacology and Therapeutics, Trinity College Dublin, Ireland.
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Reynhout S, Jansen S, Haesen D, van Belle S, de Munnik SA, Bongers EM, Schieving JH, Marcelis C, Amiel J, Rio M, Mclaughlin H, Ladda R, Sell S, Kriek M, Peeters-Scholte CM, Terhal PA, van Gassen KL, Verbeek N, Henry S, Scott Schwoerer J, Malik S, Revencu N, Ferreira CR, Macnamara E, Braakman HM, Brimble E, Ruzhnikov MR, Wagner M, Harrer P, Wieczorek D, Kuechler A, Tziperman B, Barel O, de Vries BB, Gordon CT, Janssens V, Vissers LE. De Novo Mutations Affecting the Catalytic Cα Subunit of PP2A, PPP2CA, Cause Syndromic Intellectual Disability Resembling Other PP2A-Related Neurodevelopmental Disorders. Am J Hum Genet 2019; 104:139-156. [PMID: 30595372 DOI: 10.1016/j.ajhg.2018.12.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 12/06/2018] [Indexed: 12/11/2022] Open
Abstract
Type 2A protein phosphatases (PP2As) are highly expressed in the brain and regulate neuronal signaling by catalyzing phospho-Ser/Thr dephosphorylations in diverse substrates. PP2A holoenzymes comprise catalytic C-, scaffolding A-, and regulatory B-type subunits, which determine substrate specificity and physiological function. Interestingly, de novo mutations in genes encoding A- and B-type subunits have recently been implicated in intellectual disability (ID) and developmental delay (DD). We now report 16 individuals with mild to profound ID and DD and a de novo mutation in PPP2CA, encoding the catalytic Cα subunit. Other frequently observed features were severe language delay (71%), hypotonia (69%), epilepsy (63%), and brain abnormalities such as ventriculomegaly and a small corpus callosum (67%). Behavioral problems, including autism spectrum disorders, were reported in 47% of individuals, and three individuals had a congenital heart defect. PPP2CA de novo mutations included a partial gene deletion, a frameshift, three nonsense mutations, a single amino acid duplication, a recurrent mutation, and eight non-recurrent missense mutations. Functional studies showed complete PP2A dysfunction in four individuals with seemingly milder ID, hinting at haploinsufficiency. Ten other individuals showed mutation-specific biochemical distortions, including poor expression, altered binding to the A subunit and specific B-type subunits, and impaired phosphatase activity and C-terminal methylation. Four were suspected to have a dominant-negative mechanism, which correlated with severe ID. Two missense variants affecting the same residue largely behaved as wild-type in our functional assays. Overall, we found that pathogenic PPP2CA variants impair PP2A-B56(δ) functionality, suggesting that PP2A-related neurodevelopmental disorders constitute functionally converging ID syndromes.
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Tang S, Liu Y, Wang X, Liang Z, Cai H, Mo L, Xiao D, Guo S, Ouyang Y, Sun B, Lu C, Li X. Characterization of overexpression of the alternatively spliced isoform of the protein phosphatase 2A catalytic subunit in cells. Biochem Biophys Res Commun 2017; 494:491-498. [PMID: 29066346 DOI: 10.1016/j.bbrc.2017.10.093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 10/17/2017] [Indexed: 12/18/2022]
Abstract
PP2Acα2 is a recently discovered PP2Acα alternative splicing isoform that can be induced following serum withdrawal. It shows enhanced binding to immunoglobulin binding protein 1 and is overexpressed in chronic lymphocytic leukemia patients. Current knowledge concerning PP2Acα2 is limited. In this study, we induced and cloned PP2Acα2 from HL-60 cells and human lymphocytes, transfected them into human embryonic kidney 293 cells and constructed a stable overexpression cell line. We found that PP2Acα2 mRNA inhibits expression of its longer isoform PP2Acα mRNA but had no effect on the final protein expression and modification of this longer isoform. Moreover, PP2Acα2-overexpressed cells demonstrated increased expression of IGBP1, activated mTORC1 signaling to reduce basal autophagy and increased anchorage-independent growth. Our study provides new insights into the complex mechanisms of PP2A regulation.
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Affiliation(s)
- Shen Tang
- School of Preclinical medicine, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Yuyang Liu
- Hunan Provincial Center for Disease Control and Prevention, Changsha, Hunan, 410005, China
| | - Xinhang Wang
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, China; School of Public Health, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Ziwei Liang
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, China; School of Public Health, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Haiqing Cai
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, China; School of Public Health, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Laiming Mo
- School of Preclinical medicine, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Deqiang Xiao
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, China
| | - Songchao Guo
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, China
| | - Yiqiang Ouyang
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, China
| | - Bin Sun
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, China; School of Public Health, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Cailing Lu
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, China; School of Public Health, Guangxi Medical University, Nanning, Guangxi, 530021, China.
| | - Xiyi Li
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, China; School of Public Health, Guangxi Medical University, Nanning, Guangxi, 530021, China.
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Crystal structure of the human Tip41 orthologue, TIPRL, reveals a novel fold and a binding site for the PP2Ac C-terminus. Sci Rep 2016; 6:30813. [PMID: 27489114 PMCID: PMC4973239 DOI: 10.1038/srep30813] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 07/08/2016] [Indexed: 11/25/2022] Open
Abstract
TOR signaling pathway regulator-like (TIPRL) is a regulatory protein which inhibits the catalytic subunits of Type 2A phosphatases. Several cellular contexts have been proposed for TIPRL, such as regulation of mTOR signaling, inhibition of apoptosis and biogenesis and recycling of PP2A, however, the underlying molecular mechanism is still poorly understood. We have solved the crystal structure of human TIPRL at 2.15 Å resolution. The structure is a novel fold organized around a central core of antiparallel beta-sheet, showing an N-terminal α/β region at one of its surfaces and a conserved cleft at the opposite surface. Inside this cleft, we found a peptide derived from TEV-mediated cleavage of the affinity tag. We show by mutagenesis, pulldown and hydrogen/deuterium exchange mass spectrometry that this peptide is a mimic for the conserved C-terminal tail of PP2A, an important region of the phosphatase which regulates holoenzyme assembly, and TIPRL preferentially binds the unmodified version of the PP2A-tail mimetic peptide DYFL compared to its tyrosine-phosphorylated version. A docking model of the TIPRL-PP2Ac complex suggests that TIPRL blocks the phosphatase’s active site, providing a structural framework for the function of TIPRL in PP2A inhibition.
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Grech G, Baldacchino S, Saliba C, Grixti MP, Gauci R, Petroni V, Fenech AG, Scerri C. Deregulation of the protein phosphatase 2A, PP2A in cancer: complexity and therapeutic options. Tumour Biol 2016; 37:11691-11700. [PMID: 27444275 DOI: 10.1007/s13277-016-5145-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 07/11/2016] [Indexed: 01/26/2023] Open
Abstract
The complexity of the phosphatase, PP2A, is being unravelled and current research is increasingly providing information on the association of deregulated PP2A function with cancer initiation and progression. It has been reported that decreased activity of PP2A is a recurrent observation in many types of cancer, including colorectal and breast cancer (Baldacchino et al. EPMA J. 5:3, 2014; Cristobal et al. Mol Cancer Ther. 13:938-947, 2014). Since deregulation of PP2A and its regulatory subunits is a common event in cancer, PP2A is a potential target for therapy (Baldacchino et al. EPMA J. 5:3, 2014). In this review, the structural components of the PP2A complex are described, giving an in depth overview of the diversity of regulatory subunits. Regulation of the active PP2A trimeric complex, through phosphorylation and methylation, can be targeted using known compounds, to reactivate the complex. The endogenous inhibitors of the PP2A complex are highly deregulated in cancer, representing cases that are eligible to PP2A-activating drugs. Pharmacological opportunities to target low PP2A activity are available and preclinical data support the efficacy of these drugs, but clinical trials are lacking. We highlight the importance of PP2A deregulation in cancer and the current trends in targeting the phosphatase.
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Affiliation(s)
- Godfrey Grech
- Department of Pathology, Faculty of Medicine & Surgery, Medical School, University of Malta, Msida, MSD2090, Malta.
| | - Shawn Baldacchino
- Department of Pathology, Faculty of Medicine & Surgery, Medical School, University of Malta, Msida, MSD2090, Malta
| | - Christian Saliba
- Centre for Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Maria Pia Grixti
- Department of Pathology, Faculty of Medicine & Surgery, Medical School, University of Malta, Msida, MSD2090, Malta
| | - Robert Gauci
- Department of Pathology, Faculty of Medicine & Surgery, Medical School, University of Malta, Msida, MSD2090, Malta
| | - Vanessa Petroni
- Department of Anatomy, Faculty of Medicine & Surgery, University of Malta, Msida, Malta
| | - Anthony G Fenech
- Department of Clinical Pharmacology & Therapeutics, Faculty of Medicine & Surgery, University of Malta, Msida, Malta
| | - Christian Scerri
- Department of Physiology and Biochemistry, Faculty of Medicine & Surgery, University of Malta, Msida, Malta.,Molecular Genetics Clinic, Mater Dei Hospital, Msida, Malta
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Evaluation of Caspase-9b and PP2Acα2 as potential biomarkers for chronic lymphocytic leukemia. Biomark Res 2016; 4:9. [PMID: 27152197 PMCID: PMC4857392 DOI: 10.1186/s40364-016-0063-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 04/26/2016] [Indexed: 11/17/2022] Open
Abstract
Background Disruption of alternative splicing in apoptotic factors has been associated to chronic lymphocytic leukemia among other cancers and hematological malignancies. The proapoptotic proteins Caspase-9 and PP2Acα are functionally related in a direct interaction, which constitutes a promising target for cancer therapy. Both proteins present aberrant mRNA splicing variants that are antiapoptotic (Caspase-9b) and catalytically inactive (PP2Acα2), respectively. Results In this work we have analyzed the relative abundance of the aberrant spliced forms Caspase-9b and PP2Acα2 in several cell lines and chronic lymphocytic leukemia patients and correlated it with several parameters of the disease. Despite 40 % of the patients presented Caspase-9b dysregulation, there was no direct association between alterations in Caspase-9b relative abundance and the parameters analyzed in medical records. More importantly, PP2Acα2 dysregulation was observed in 88 % of CLL patients and was related with advanced stages of the malignancy. Conclusions Caspase-9b dysregulation seemed to be associated with the disease, although the differences between healthy donors and CLL patients were not statistically significant. However, PP2Acα2 dysregulation was significantly different between healthy donors and CLL patients and correlated with Binet B and C stages; therefore, we propose the use of PP2Acα2 dysregulation as a potential biomarker for advanced stages of chronic lymphocytic leukemia.
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8
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Wang J, Li Z, Liu B, Chen G, Shao N, Ying X, Wang Y. Systematic study of cis-antisense miRNAs in animal species reveals miR-3661 to target PPP2CA in human cells. RNA (NEW YORK, N.Y.) 2016; 22:87-95. [PMID: 26577378 PMCID: PMC4691837 DOI: 10.1261/rna.052894.115] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 10/03/2015] [Indexed: 05/13/2023]
Abstract
MicroRNAs (miRNAs) suppress targeting gene expression through blocking translation or triggering mRNA degradation and, in general, act in trans, through a partially complementary interaction with the 3' untranslated region (3' UTR) or coding regions of a target gene. Although it has been reported previously that some miRNAs suppress their target genes on the opposite strand with a fully complementary sequence (i.e., natural antisense miRNAs that act in cis), there is no report to systematically study such cis-antisense miRNAs in different animal species. Here we report that cis-antisense miRNAs do exist in different animal species: 48 in Caenorhabditis elegans, 17 in Drosophila, 36 in Mus musculus, and 52 in Homo sapiens using a systematical bioinformatics approach. We show that most of these cis-antisense miRNAs can efficiently reduce the expression levels of their target genes in human cells. We further investigate hsa-miR-3661, one of the predicted cis-antisense miRNAs, in detail and demonstrate that this miRNA directly targets the coding sequence of PPP2CA located on the opposite DNA strand and inhibits the PPP2CA expression. Taken together, these results indicate that cis-antisense miRNAs are conservative and functional in animal species including humans.
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Affiliation(s)
- Jian Wang
- Department of Radiation Oncology, Emory University School of Medicine, Winship Cancer Institute of Emory University, Atlanta, Georgia 30322, USA
| | - Zongcheng Li
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Bailong Liu
- Department of Radiation Oncology, Emory University School of Medicine, Winship Cancer Institute of Emory University, Atlanta, Georgia 30322, USA The First Norman Bethune Hospital of Jilin University, Changchun 130012, China
| | - Guangnan Chen
- Department of Radiation Oncology, Emory University School of Medicine, Winship Cancer Institute of Emory University, Atlanta, Georgia 30322, USA
| | - Ningsheng Shao
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Xiaomin Ying
- Beijing Institute of Basic Medical Sciences, Beijing 100850, China
| | - Ya Wang
- Department of Radiation Oncology, Emory University School of Medicine, Winship Cancer Institute of Emory University, Atlanta, Georgia 30322, USA
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Rack JGM, VanLinden MR, Lutter T, Aasland R, Ziegler M. Constitutive nuclear localization of an alternatively spliced sirtuin-2 isoform. J Mol Biol 2013; 426:1677-91. [PMID: 24177535 DOI: 10.1016/j.jmb.2013.10.027] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 10/19/2013] [Accepted: 10/22/2013] [Indexed: 11/25/2022]
Abstract
Sirtuin-2 (SIRT2), the cytoplasmic member of the sirtuin family, has been implicated in the deacetylation of nuclear proteins. Although the enzyme has been reported to be located to the nucleus during G2/M phase, its spectrum of targets suggests functions in the nucleus throughout the cell cycle. While a nucleocytoplasmic shuttling mechanism has been proposed for SIRT2, recent studies have indicated the presence of a constitutively nuclear isoform. Here we report the identification of a novel splice variant (isoform 5) of SIRT2 that lacks a nuclear export signal and encodes a predominantly nuclear isoform. This novel isoform 5 fails to show deacetylase activity using several assays, both in vitro and in vivo, and we are led to conclude that this isoform is catalytically inactive. Nevertheless, it retains the ability to interact with p300, a known interaction partner. Moreover, changes in intrinsic tryptophan fluorescence upon denaturation indicate that the protein is properly folded. These data, together with computational analyses, confirm the structural integrity of the catalytic domain. Our results suggest an activity-independent nuclear function of the novel isoform.
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Affiliation(s)
- Johannes G M Rack
- Department of Molecular Biology, University of Bergen, Postbox 7803, 5020 Bergen, Norway.
| | - Magali R VanLinden
- Department of Molecular Biology, University of Bergen, Postbox 7803, 5020 Bergen, Norway.
| | - Timo Lutter
- Department of Molecular Biology, University of Bergen, Postbox 7803, 5020 Bergen, Norway.
| | - Rein Aasland
- Department of Molecular Biology, University of Bergen, Postbox 7803, 5020 Bergen, Norway.
| | - Mathias Ziegler
- Department of Molecular Biology, University of Bergen, Postbox 7803, 5020 Bergen, Norway.
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